Variants of SARS-CoV-2

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Positive, negative, and neutral mutations during the evolution of coronaviruses like SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has a lot of variants. Some of them are important because of increased transmission and vaccines being less effective on them.[1][2] This article discusses relevant variants of SARS-CoV-2 and mutations in these variants.

The variant WIV04/2019 is most closely related to the original virus when it began infecting humans.[3]

Overview[change | change source]

There are a lot of lineages of SARS-CoV-2.[4] Lineages are variants that are genetically the same.

Nomenclature[change | change source]

SARS-CoV-2 corresponding nomenclatures[5]
PANGO lineages[6] Notes to PANGO lineages[7] Nextstrain clades,[8] 2021[9] GISAID clades Notable variants
A.1–A.6 19B S contains "reference sequence" WIV04/2019[3]
B.3–B.7, B.9, B.10, B.13–B.16 19A L
O[a]
B.2 V
B.1 B.1.5–B.1.72 20A G Lineage B.1 in the PANGO Lineages nomenclature system
B.1.9, B.1.13, B.1.22, B.1.26, B.1.37 GH
B.1.3–B.1.66 20C Includes Lineage B.1.429 / CAL.20C[10] and Lineage B.1.525[11]
20G Predominant in US generally, Jan '21[10]
20H Includes B.1.351 aka 20H/501Y.V2 or 501.V2 lineage
B.1.1 20B GR Includes B.1.1.207[source?]
20D
20J Includes P.1 and P.2[12][13]
20F
20I Includes lineage B.1.1.7 aka VOC-202012/01, VOC-20DEC-01 or 20I/501Y.V1
B.1.177 20E (EU1)[9] GV[a] Derived from 20A[9]

There's no consistent nomenclature for SARS-CoV-2.[15] Variants are usually refered to by the country where the variant came from.[16][17][18] For example, B.1.1.7 is usually called the "UK variant."

Criteria for importance[change | change source]

Viruses generally mutate over time, creating new variants. When a new variant grows in a population, it's labeled as an "emerging variant".

Some of the potential consequences of emerging variants are the following:[19][20]

  • Increased transmissibility
  • Increased Morality (death).
  • Ability to evade natural immunity (e.g., causing reinfections)
  • Ability to infect vaccinated people

Notable variants[change | change source]

Cluster 5[change | change source]

In early November 2020, Cluster 5, also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI),[21] was discovered in Northern Jutland, Denmark, and is believed to have been spread from minks to humans via mink farms. On 4 November 2020, it was announced that the mink population in Denmark would be culled to prevent the possible spread of this mutation and reduce the risk of new mutations happening. A lockdown and travel restrictions were introduced in seven municipalities of Northern Jutland to prevent the mutation from spreading, which could compromise national or international responses to the COVID-19 pandemic. By 5 November 2020, some 214 mink-related human cases had been detected.[22]

The World Health Organization (WHO) has stated that cluster 5 has a "moderately decreased sensitivity to neutralizing antibodies".[23] SSI warned that the mutation could reduce the effect of COVID-19 vaccines under development, although it was unlikely to render them useless. Following the lockdown and mass-testing, SSI announced on 19 November 2020 that cluster 5 in all probability had become extinct.[24] As of 1 February 2021, authors to a peer-reviewed paper, all of whom were from the SSI, assessed that cluster 5 was not in circulation in the human population.[25]

Lineage B.1.1.7 / Variant of Concern 20DEC-01[change | change source]

False-colour transmission electron micrograph of a B.1.1.7 variant coronavirus. The variant's increased transmissibility is believed to be due to changes in structure of the spike proteins, shown here in green.

This variant was first detected in October 2020 during the COVID-19 pandemic in the United Kingdom from a sample taken the month before in Kent.[26] Lineage B.1.1.7,[27] It's correlated with a big increase in COVID-19 infection in United Kingdom, partly because of the N501Y mutation.[28] There is some evidence that this variant has 40%–80% increased transmissibility and an increase in deadliness.[29][30]

Variant of Concern 21FEB-02[change | change source]

Variant of Concern 21FEB-02 (previously written as VOC-202102/02), described by Public Health England (PHE) as "B.1.1.7 with E484K"[31] is the B.1.1.7 variant with an additional E484K mutation. As of 17 March 2021, there are 39 confirmed cases of VOC-21FEB-02 in the UK.[31] On 4 March 2021, scientists reported B.1.1.7 with E484K mutations in the state of Oregon. It seems that this combination happened randomly in Oregon, instead of coming from the UK.

Lineage B.1.1.317[change | change source]

B.1.1.317 is not a variant of concern, but Queensland Health forced 2 people in hotel quarantine in Brisbane, Australia to go through an extra 5 days quarantine on top of the mandatory 14 days after it was confirmed they were infected with this variant.[32]

Lineage B.1.1.318[change | change source]

Lineage B.1.1.318 was detected on 24 February 2021. 16 cases of it have been detected in the UK.[31][33]

Lineage B.1.351[change | change source]

On 18 December 2020, the 501.V2 variant, also known as 501.V2, 20H/501Y.V2 (formerly 20C/501Y.V2), VOC-20DEC-02 (formerly VOC-202012/02), or lineage B.1.351,[19] was first detected in South Africa and reported by the country's health department.[34] Researchers and officials reported that the variant is more likely to make young people very sick.[35][36] The South African health department also said that the variant may be driving the second wave of the COVID-19 epidemic in the country.[34][35]

Scientists said that the variant has many mutations that allow it to attach more easily to human cells because of the following three mutations in the receptor-binding domain (RBD) in the spike glycoprotein of the virus: N501Y,[34][37] K417N, and E484K.[38][39] The N501Y mutation has also been detected in the United Kingdom.[34][40]

Lineage B.1.429 / CAL.20C[change | change source]

Lineage B.1.429, also known as CAL.20C, has by five distinct mutations (I4205V and D1183Y in the ORF1ab-gene, and S13I, W152C, L452R in the spike proteins S-gene).[10][41] B.1.429 might be more transmissible.[41] The CDC has listed B.1.429 and the related B.1.427 as "variants of concern," and says that they have a ~20% increase in transmissibility.

B.1.429 was first discovered in July 2020 by researchers at the Cedars-Sinai Medical Center, California, in one of 1,230 virus samples collected in Los Angeles County since the start of the COVID-19 epidemic.[42] It wasn't detected again until September when it reappeared among samples in California, but numbers remained very low until November.[43][44] In November 2020, the CAL.20C variant accounted for 36 percent of samples collected at Cedars-Sinai Medical Center, and by January 2021, the CAL.20C variant was 50 percent of samples.[41]

Lineage B.1.525[change | change source]

B.1.525, also called VUI-21FEB-03[31] (previously VUI-202102/03) by Public Health England (PHE) and formerly known as UK1188,[31] doesn't have the same N501Y mutation found in B.1.1.7, 501.V2 and P.1, but has the same E484K-mutation as found in the P.1, P.2, and 501.V2 variants.[45] B.1.525 is different from all other variants by having both the E484K-mutation and a new F888L mutation. As of March 5, it had been found in 23 countries, including the UK, Denmark, Finland, Norway, Netherlands, Belgium, France, Spain, Nigeria, Ghana, Jordan, Japan, Singapore, Australia, Canada, Germany, Italy, Slovenia, Austria, Malaysia, Switzerland, the Republic of Ireland and the US.[46][47][48][49][50][51][52]

Lineage P.1[change | change source]

Lineage P.1, termed Variant of Concern 21JAN-02[31] (formerly VOC-202101/02) by Public Health England[31] and 20J/501Y.V3 by Nextstrain,[11] was found in Tokyo on 6 January 2021 by the National Institute of Infectious Diseases (NIID). The new lineage was first identified in four people who arrived in Tokyo having travelled from the Brazilian Amazonas state on 2 January 2021.[53] On 12 January 2021, the Brazil-UK CADDE Centre confirmed 13 local cases of the P.1 new lineage in the Amazon rain forest.[54] This variant of SARS-CoV-2 has been named P.1 lineage (although it is a descendant of B.1.1.28, the name B.1.1.28.1 is not permitted and thus the resultant name is P.1), and has 17 unique amino acid changes, 10 of which in its spike protein, including the three concerning mutations: N501Y, E484K and K417T.[54][55][56][57]

A study of samples from Manaus between November 2020 and January 2021, showed the P.1 lineage to be 1.4–2.2 times more transmissible. The variant is also 10–80% more deadly.[58][59][60]

A vaccinated person has a higher risk of getting a mild P.1 infection while still being 100% protected against hospitalisation or death.[61]

Preliminary data from two studies indicate that the Oxford–AstraZeneca vaccine is effective against the P.1 variant, although the exact level of efficacy has not yet been released.[62][63] Preliminary data from a study conducted by Instituto Butantan suggest that CoronaVac is effective against the P.1 variant as well, and the study will be expanded to obtain definitive data.[64]

Differential vaccine effectiveness[change | change source]

Notes[change | change source]

  1. 1.0 1.1 In another source, GISAID name a set of 7 clades without the O clade but including a GV clade.[14]

Cite error: Cite error: <ref> tag with name "Nextstrain criteria" defined in <references> is not used in prior text. ().

References[change | change source]

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  2. Kupferschmidt, Kai (15 January 2021). "New coronavirus variants could cause more reinfections, require updated vaccines". Science. American Association for the Advancement of Science. doi:10.1126/science.abg6028. Retrieved 2 February 2021.
  3. 3.0 3.1 Zhukova, Anna; Blassel, Luc; Lemoine, Frédéric; Morel, Marie; Voznica, Jakub; Gascuel, Olivier (24 November 2020). "Origin, evolution and global spread of SARS-CoV-2". Comptes Rendus Biologies: 1–20. doi:10.5802/crbiol.29. PMID 33274614. Archived from the original on 21 February 2021. Retrieved 6 April 2021.
  4. "Lineage descriptions". cov-lineages.org. Pango team.
  5. This table is an adaptation and expansion of Alm et al., figure 1.
  6. Rambaut, A.; Holmes, E.C.; O’Toole, Á.; et al. (2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMID 32669681. S2CID 220544096. Cited in Alm et al.
  7. Alm, E.; Broberg, E. K.; Connor, T.; Hodcroft, E. B.; Komissarov, A. B.; Maurer-Stroh, S.; et al. (2020). "Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020". Euro Surveillance. 25 (32). doi:10.2807/1560-7917.ES.2020.25.32.2001410. PMC 7427299. PMID 32794443.
  8. "Nextclade" (What are the clades?). clades.nextstrain.org. Archived from the original on 19 January 2021. Retrieved 19 January 2021.
  9. 9.0 9.1 9.2 9.3 Bedford, Trevor; Hodcroft, Emma B; Neher, Richard A (6 January 2021). "Updated Nextstrain SARS-CoV-2 clade naming strategy". nextstrain.org/blog. Retrieved 19 January 2021.
  10. 10.0 10.1 10.2 Zhang, Wenjuan; Davis, Brian D.; Chen, Stephanie S.; Martinez, Jorge M Sincuir; Plummer, Jasmine T.; Vail, Eric (2021). "Emergence of a novel SARS-CoV-2 strain in Southern California, USA". doi:10.1101/2021.01.18.21249786. S2CID 231646931. Cite journal requires |journal= (help)
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  12. "PANGO lineages-Lineage B.1.1.28". cov-lineages.org. Retrieved 4 February 2021.[not in the source given]
  13. "Variant: 20J/501Y.V3". covariants.org. 1 April 2021. Retrieved 6 April 2021.
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  18. For a list of sources using names referring to the country in which the variants were first identified, see, for example, Talk:South African COVID variant and Talk:U.K. Coronavirus variant.
  19. 19.0 19.1 "Emerging SARS-CoV-2 Variants". cdc.org (Science brief). Centers for Disease Control and Prevention. 28 January 2021. Retrieved 4 January 2021. This article incorporates text from this source, which is in the public domain.
  20. Contributor, IDSA (2 February 2021). "COVID "Mega-variant" and eight criteria for a template to assess all variants". Science Speaks: Global ID News. Retrieved 20 February 2021.
  21. Lassaunière, Ria; Fonager, Jannik; Rasmussen, Morten; Frische, Anders; Strandh, Charlotta; Rasmussen, Thomas; et al. (10 November 2020). SARS-CoV-2 spike mutations arising in Danish mink, their spread to humans and neutralization data (Preprint). Statens Serum Institut. Archived from the original on 10 November 2020. Retrieved 11 November 2020.
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  23. Cite error: The named reference WHO was used but no text was provided for refs named (see the help page).
  24. Cite error: The named reference sum19nov was used but no text was provided for refs named (see the help page).
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  27. Chand, Meera; Hopkins, Susan; Dabrera, Gavin; Achison, Christina; Barclay, Wendy; Ferguson, Neil; Volz, Erik; Loman, Nick; Rambaut, Andrew; Barrett, Jeff (21 December 2020). Investigation of novel SARS-COV-2 variant: Variant of Concern 202012/01 (PDF) (Report). Public Health England. Retrieved 23 December 2020.
  28. "New evidence on VUI-202012/01 and review of the public health risk assessment". Retrieved 4 January 2021.
  29. Gallagher, James (22 January 2021). "Coronavirus: UK variant 'may be more deadly'". BBC News. Retrieved 22 January 2021.
  30. Peter Horby, Catherine Huntley, Nick Davies, John Edmunds, Neil Ferguson, Graham Medley, Andrew Hayward, Muge Cevik, Calum Semple (11 February 2021). "NERVTAG paper on COVID-19 variant of concern B.1.1.7: NERVTAG update note on B.1.1.7 severity (2021-02-11)" (PDF). www.gov.uk.CS1 maint: multiple names: authors list (link)
  31. 31.0 31.1 31.2 31.3 31.4 31.5 31.6 "Variants: distribution of cases data". gov.uk. Government Digital Service.
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  33. "Latest update: New Variant Under Investigation designated in the UK". www.gov.uk. 4 March 2021. Retrieved 5 March 2021.
  34. 34.0 34.1 34.2 34.3 "South Africa announces a new coronavirus variant". The New York Times. 18 December 2020. Retrieved 20 December 2020.
  35. 35.0 35.1 Wroughton, Lesley; Bearak, Max (18 December 2020). "South Africa coronavirus: Second wave fueled by new strain, teen 'rage festivals'". The Washington Post. Retrieved 20 December 2020.
  36. "Update on Covid-19 (18th December 2020)". Press release. 18 December 2020. https://sacoronavirus.co.za/2020/12/18/update-on-covid-19-18th-december-2020/. Retrieved 2020-12-23. "Our clinicians have also warned us that things have changed and that younger, previously healthy people are now becoming very sick." 
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  38. Lowe, Derek (22 December 2020). "The New Mutations". In the Pipeline. American Association for the Advancement of Science. Retrieved 23 December 2020. I should note here that there's another strain in South Africa that is bringing on similar concerns. This one has eight mutations in the Spike protein, with three of them (K417N, E484K and N501Y) that may have some functional role.
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  41. 41.0 41.1 41.2 "New California Variant May Be Driving Virus Surge There, Study Suggests". New York Times. 19 January 2021.
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